# An R package to Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences (from RNA-seq data)

## Documentation for package ‘IsoformSwitchAnalyzeR’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

analyzeAlternativeSplicing | Analyse alternative splicing (including intron retention(s))
analyzeCPAT | Import Result of External Sequence Analysis
analyzeIntronRetention | Analyse alternative splicing (including intron retention(s))
analyzeORF | Predictiction of Transcript Open Reading Frame.
analyzePFAM | Import Result of PFAM analysis
analyzeSignalP | Import Result of SignalP Analysis
analyzeSwitchConsequences | Analyze Consequences of Isoform Switches
CDSSet | Container for coding sequence (CDS) annotation information
CDSSet-class | Container for coding sequence (CDS) annotation information
createSwitchAnalyzeRlist | Create a switchAnalyzeRlist Object
exampleSwitchList | Example data for IsoformSwitchAnalyzeR
exampleSwitchListAnalyzed | Example data for IsoformSwitchAnalyzeR
exampleSwitchListIntermediary | Example data for IsoformSwitchAnalyzeR
extractConsequenceEnrichment | Analyze data for enrichment of specific consequences
extractConsequenceEnrichmentComparison | Compare enrichment of specific consequences between comparisons
extractConsequenceGenomeWide | Genome wide Analysis of Consequences due to isoform switching
extractConsequenceSummary | Analyze Switch Consequences
extractExpressionMatrix | Extract Gene/Isoform Expression Matrix.
extractGenomeWideAnalysis | Genome wide Analysis of Consequences due to isoform switching
extractSequence | Extract nucloetide (and amino acid) sequence of transcripts.
extractSplicingEnrichment | Analyze data for enrichment of specific type of alternative splicing
extractSplicingEnrichmentComparison | Compare enrichment of specific type of alternative splicing between comparisons
extractSplicingGenomeWide | Genome wide Analysis of alternative splicing
extractSplicingSummary | Exracts alternative splicing summary
extractSwitchOverlap | Visualize Switch Overlap
extractSwitchSummary | Summarize Isoform Switches test Result.
extractTopSwitches | Extract Top Isoform Switches.
getCDS | Retrieve CDS information from UCSC
importCufflinksFiles | Import CuffDiff (Cufflinks) Data Into R
importGTF | Import Transcripts from a GTF file into R
importIsoformExpression | Import expression data from Kallisto, Salmon, RSEM or StringTie into R.
importRdata | Create SwitchAnalyzeRlist From Standard R Objects
isoformSwitchAnalysisCombined | Isoform Switch Analysis Workflow: Extract, Annoate and Visualize all Significant Isoform Swtiches
isoformSwitchAnalysisPart1 | Isoform Switch Analysis Workflow Part 1: Extract Isoform Switches and Their Sequences
isoformSwitchAnalysisPart2 | Isoform Switch Analysis Workflow Part 2: Plot All Isoform Switches and Their Annotation
isoformSwitchTestDEXSeq | Statistical Test for identifying Isoform Switching via DEXSeq
isoformSwitchTestDRIMSeq | Statistical Test for identifying Isoform Switching via DRIMSeq.
isoformToGeneExp | Summarize isoform expression to gene level expression.
isoformToIsoformFraction | Calculate isoform fraction from isoform abundance matrix
preFilter | Filtering of a switchAnalyzeRlist
removeAnnoationData | Removes data not needed after switch identification.
subsetSwitchAnalyzeRlist | A function which subset all enteries in a switchAnalyzeRlist.
switchAnalyzeRlist | Create a switchAnalyzeRlist Object
switchAnalyzeRlist-class | Create a switchAnalyzeRlist Object
switchPlot | Isoform Switch Analysis Plot
switchPlotGeneExp | Plots for Analyzing Expression and Isoform Usage
switchPlotIsoExp | Plots for Analyzing Expression and Isoform Usage
switchPlotIsoUsage | Plots for Analyzing Expression and Isoform Usage
switchPlotTopSwitches | Creating the Isoform Switch Analysis Plot for the Top Switches
switchPlotTranscript | Plot Transcript Structure and Annoation